Protein Modeling C

[kwijiborjt]

Unfortunately we will be using the online version. It was much easier for the IT guy at west point to set it up that way. I hope it doesn't pose too much of an inconvenience.

My favored function for displaying a side chain is selecting the desired residues (select (#) or select*(chainletter) and first#-last#), and then ordering 'wireframe 200'. The number you choose affects how large the side chain is displayed.

I wasn't aware that this region of DNA was methylated at all... *checking jmol*.

[kwijiborjt]

Big Question!

Despite my frequent searches, I can't seem to find any information on which amino acid sidchains methylate the Cytosine in the DNA sequence. The closest I've come to is Leucine's double-branched methyl group. The problem though is that only one Leucine sidechain faces toward the actual DNA molecule because of the molecules polarity. Therefore I can't be certian that Leucine's sidechain is causing the reaction. So: which amino acids are important for DNA alteration?


TL;DR- Which amino acids function to methylate (enact upon) the DNA?

I don't see any methylated cytosines in the klf4 file. If you do, give me the residue name and i'll check it out. As a general rule, hydrocarbon chains are not reactive (e.g., a leucine side chain), therefore it's unlikely that this would be methylating anything.

http://en.wikipedia.org/wiki/5-methylcytosine

I don't know the biochemical mechanism of a DNA methyltransferase, but if you're suggesting that some side chain on Klf4 is methylating the DNA, i would say that this is definitely not the case.

http://en.wikipedia.org/wiki/DNA_methyltransferase

[nanowhale]

One last thing.... I am out of ideas for the pre-build add-ons, anyone have some ideas I could use?

[Phenylethylamine]

I had forgotten from last year how much the state test focuses on the on-site build protein (especially the long answer questions). We could probably have been a bit more prepared on that front than we were.

Also, I met a few of you- kwijiborjt, I think, and I'm not sure who I talked to on stage. Thank you for your enthusiasm; I'm glad my advice was helpful

[bloopy]

Hey guys, I need a bit of help as to how exactly to study for the test part of this event. I did absolutely horrible on the Regionals test, even though I had pretty much gone through all the links and videos related to the stem cells and zinc fingers specifically (a lot of these showed up on the test, which I was happy to see). However, there was a lot of stuff about nucleosomes and chromatin in the test too, which completely caught me off guard and sunk the event, and I was just wondering what general knowledge of proteins that people are studying? Right now I'm planning to read more into the transcription process itself, and I'm also thinking of studying meiosis and protein synthesis.

Also, does anybody have a good link that explains as to how, specifically, these transcription factors revert the cell back into a pluripotent state? Can't find this information anywhere.

[kwijiborjt]

A more effective way to study would be to read extensively about the topic and study science concepts that are relevant to iPS cells in general and also to the structure and function of the assigned proteins.

This is also a good principle to guide your creative additions. There were a lot of wonderful additions that people clearly put a lot of work into, but they didn't receive credit if they didn't elaborate the relationship between the structure of Klf4 and its function. At least, that was how I judged. Your states may judge differently. But, for example, under my judging scheme a scale model of a retrovirus, while beautiful, didn't get you extra points.

Edit: However, for last year I would have counted a model of a flu particle as a creative addition, had it shown hemagglutinin and neuraminidase on the surface of that flu particle. That's because the fact that they're transmembrane surface proteins is important to their function.

[Phenylethylamine]

This is also a good principle to guide your creative additions. There were a lot of wonderful additions that people clearly put a lot of work into, but they didn't receive credit if they didn't elaborate the relationship between the structure of Klf4 and its function. At least, that was how I judged. Your states may judge differently. But, for example, under my judging scheme a scale model of a retrovirus, while beautiful, didn't get you extra points.

How specific are the scoring guidelines given to the judges? Also, is it still the case- as it was last year- that a model can get credit for up to four creative additions? (Sub-question of that last one: what counts as "one" creative addition? E.g., I have DNA represented in my model; I also have certain DNA bases represented. That doesn't seem like two full, separate creative additions to me, but it's really two different concepts: DNA binding, and specificity. So would it be scored as one creative addition, or two?)

Also, a belated congratulations; I assume you're the former-competitor-turned-supervisor who the lady handing out medals referred to as having "won the event in the past". I didn't know this had been an event prior to last year.

[nanowhale]

It was still a trial event prior but not many states used it, my coach had the kit for it from before last year.

[kwijiborjt]

I modified the rubric handed down from on high. The rubric they gave me had four additions suggested and gave latitude for up to 3 points each for any other additions at my discretion. There is a cap on how many creative addition points you can get. Under their scheme it was 12, under mine it was 13. But it would be advisable to do more than four creative additions because you likely won't get full points on each one of them (unless you're as obsessed with accuracy as I am!).

For your model, you actually got a point on my scheme that no other team got. I had a criterion in my DNA category, "bases modeled to demonstrate binding". That is, you didn't get points just for modeling DNA with bases, but you did get a point if you modeled the bases in such a way that you related them to hydrogen bonding with Klf4. Since you picked out five of the bases that were involved with binding (i think there may have been one or two more if you look in jmol), you got that point. Alternately, you could have showed the appropriate arginine residues and some lysines hydrogen bonding to those bases, which would have gotten you even more points.

Bottom line, always relate structure to function, and do it with obsessive, atomic accuracy, and you will get tons of points from me. For example, i had points in my scheme for showing histidine and cysteine side chains pointed correctly (histidine with the distal nitrogen atom chelating the zinc ion and with the large side of the ring pointing radially out of the finger, and the small side pointing in, and the cysteines deflected parallel to each other away from the zinc ion). Yes, be *that* accurate. All the info is in the jmol file. Other event supervisors might not be as much of a nut job as I am, but it's things like those that make a really awesome model.

Also they must have been talking about someone else... protein modeling wasn't around when I was in high school. And they probably weren't talking about protein modeling, because my high school won last year (pride! also, i was just their coach, not the event supervisor last year) and we didn't make it to states this year . I, sadly, never got a 1st place at states, but having run an event and seen how minimal some of the margins are makes me feel a little better about that.

[Flavorflav]

Also, a belated congratulations; I assume you're the former-competitor-turned-supervisor who the lady handing out medals referred to as having "won the event in the past". I didn't know this had been an event prior to last year.

I think it was the Astronomy supervisor that they were talking about.