Protein Modeling C

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Re: Protein Modeling C

Post by Phenylethylamine »

dolphin0922 wrote:Is the side chain Asp175 significant? It seems like it becomes activated if this is cleaved, but I am not sure.
I assume you mean ASP175 in XIAP, because I can't find any other ASP175 among this year's proteins. I haven't seen anything referring to the importance of ASP175, but that doesn't mean it isn't important.

It would not be involved in cleavage/activation of XIAP, because XIAP is an inhibitor of caspase-3, and is not caspase-activated. It doesn't get cleaved during any of the processes we're interested in for the purpose of the event.
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Re: Protein Modeling C

Post by TheWiseGirl »

Phenylethylamine wrote:
gsheni wrote:Why does Chain F of XIAP
http://www.pdb.org/pdb/explore/remediat ... all&page=2
Have a huge gap from 169 - 179 ?
what can i do about it if I am modeling that chain?
The gap is just an area that they couldn't resolve properly in the x-ray crystallography. Model chain F based on the structure of chain E – they're identical.
TheWiseGirl wrote:Does anybody know what a linker peptide is? I can't seem to find a straightforward explanation on google...
The reason you can't find a straightforward explanation is because it's not a specific thing – it's a pretty general phrase. It's just being used to mean a peptide (as in a series of amino acids, in this case part of a protein) that links two sections of the protein.
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Re: Protein Modeling C

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TheWiseGirl wrote:
Phenylethylamine wrote:
gsheni wrote:Why does Chain F of XIAP
http://www.pdb.org/pdb/explore/remediat ... all&page=2
Have a huge gap from 169 - 179 ?
what can i do about it if I am modeling that chain?
The gap is just an area that they couldn't resolve properly in the x-ray crystallography. Model chain F based on the structure of chain E – they're identical.
TheWiseGirl wrote:Does anybody know what a linker peptide is? I can't seem to find a straightforward explanation on google...
The reason you can't find a straightforward explanation is because it's not a specific thing – it's a pretty general phrase. It's just being used to mean a peptide (as in a series of amino acids, in this case part of a protein) that links two sections of the protein.
Thank you! :)
No problem. Sometimes all it takes to understand something is some confidence that you actually have understood it, and it's not some novel term with different word meanings than you're used to :-)
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Re: Protein Modeling C

Post by aomdahl »

Protopedia refers to the structurally significant residues of Lys 242 and Glu 246 on Caspase-3. However, they do not appear in the the jmol based on 1i3o. so are they real- or is it another mutation on the pdb file?
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Re: Protein Modeling C

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aomdahl wrote:Protopedia refers to the structurally significant residues of Lys 242 and Glu 246 on Caspase-3. However, they do not appear in the the jmol based on 1i3o. so are they real- or is it another mutation on the pdb file?
As we've discussed before, there are two different commonly used numbering systems for caspase-3: one based on caspase-1, and the other... not. Those numbers (242 and 246) correspond to the other numbering system, the one we're not using.

The equivalent residues in our numbering system seem to be GLU379A and LYS376.
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Re: Protein Modeling C

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Does anybody know if at State there is a limit on the number of points we can receive for our prebuild in terms of creative additions? I know at nats the max is 4 creative additions, for a total of 16 points.
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Re: Protein Modeling C

Post by Phenylethylamine »

TheWiseGirl wrote:Does anybody know if at State there is a limit on the number of points we can receive for our prebuild in terms of creative additions? I know at nats the max is 4 creative additions, for a total of 16 points.
There is, as far as I can tell, some room for interpretation: yes, the maximum number of points you can get for creative additions is 16, and the most points you can get per addition is four – that's true at every level of competition – but whether that means you can only get points for up to four creative additions is unclear to me (and actually it's not clear to me if that's the way they score it at Nationals, either).

I know the NY state supervisor will give points for as many creative additions as you put on there, up to sixteen points total (e.g., if you have eight creative additions and each is good enough to get two points, there's your sixteen points; if you have six creative additions and they're each good enough for three points, you still only get sixteen... of course, more likely, you'd have something like six creative additions of which one might get 3 points, two might get two and a half points each, one gets two and a quarter points, and the remaining two each get one and a half points; partial points are a big deal in this event). I don't know specifically how models are graded at any other state competition.
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Re: Protein Modeling C

Post by TheWiseGirl »

Phenylethylamine wrote:
TheWiseGirl wrote:Does anybody know if at State there is a limit on the number of points we can receive for our prebuild in terms of creative additions? I know at nats the max is 4 creative additions, for a total of 16 points.
There is, as far as I can tell, some room for interpretation: yes, the maximum number of points you can get for creative additions is 16, and the most points you can get per addition is four – that's true at every level of competition – but whether that means you can only get points for up to four creative additions is unclear to me (and actually it's not clear to me if that's the way they score it at Nationals, either).

I know the NY state supervisor will give points for as many creative additions as you put on there, up to sixteen points total (e.g., if you have eight creative additions and each is good enough to get two points, there's your sixteen points; if you have six creative additions and they're each good enough for three points, you still only get sixteen... of course, more likely, you'd have something like six creative additions of which one might get 3 points, two might get two and a half points each, one gets two and a quarter points, and the remaining two each get one and a half points; partial points are a big deal in this event). I don't know specifically how models are graded at any other state competition.
Thanks Phenyl!! :)
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Re: Protein Modeling C

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TheWiseGirl wrote:
Phenylethylamine wrote:
TheWiseGirl wrote:Does anybody know if at State there is a limit on the number of points we can receive for our prebuild in terms of creative additions? I know at nats the max is 4 creative additions, for a total of 16 points.
There is, as far as I can tell, some room for interpretation: yes, the maximum number of points you can get for creative additions is 16, and the most points you can get per addition is four – that's true at every level of competition – but whether that means you can only get points for up to four creative additions is unclear to me (and actually it's not clear to me if that's the way they score it at Nationals, either).

I know the NY state supervisor will give points for as many creative additions as you put on there, up to sixteen points total (e.g., if you have eight creative additions and each is good enough to get two points, there's your sixteen points; if you have six creative additions and they're each good enough for three points, you still only get sixteen... of course, more likely, you'd have something like six creative additions of which one might get 3 points, two might get two and a half points each, one gets two and a quarter points, and the remaining two each get one and a half points; partial points are a big deal in this event). I don't know specifically how models are graded at any other state competition.
Thanks Phenyl!! :)
Thanks should really go to kwijiborjt (who was the NYS supervisor last year and, I assume, will be at least involved with it again this year) for letting me know all that. I don't know if he still follows this thread, but he had some very good advice in the past.
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Re: Protein Modeling C

Post by Suzumebachi »

Hey, my partner and I are doing this event for the first time; what are the red and blue end caps for? ^^;;
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