MUD transcript: 19-05-00
Tertiary Structure I
Course room(s): PPS
14:58:21 ClareS connects.
14:58:21
RamananS PPS HTTP 3m 53s 3m 32s
ClareS PPS HTTP 0s 0s
14:58:27 ClareS says "Hi"
14:58:49 ClareS says "we will wait for a few minutes to see who else turns up... I'm early for once ;)"
14:59:17 DavidM connects.
14:59:17
RamananS PPS HTTP 4m 49s 4m 28s
ClareS PPS HTTP 56s 28s
DavidM PPS HTTP 0s 0s
15:00:37 ClareS says (to DavidM) "Hello -- I'm very pleased you can join us!"
15:00:48 DavidM says "Hello everyone"
15:00:54 ClareS says "we are waiting a little while in case more students turn up"
15:01:11 ClareS says "we had four for last night's session"
15:02:23 KevinO connects.
15:02:23
RamananS PPS HTTP 7m 55s 7m 34s
ClareS PPS HTTP 4m 2s 1m 7s
DavidM PPS HTTP 3m 6s 1m 35s
KevinO PPS HTTP 0s 0s
15:04:02 ClareS says (to KevinO) "Hi"
15:04:18 RamananS says "Hello, I learnt all about GMT t9oday the hard way :)"
15:04:23 ClareS says "it would probably be a good idea to start now... others can join us when they arrive"
15:04:38 KevinO says "hi everyone"
15:05:16 ClareS says (to RamananS) "do you mean that you turned up at last night's session at the wrong time??"
15:05:38 ClareS has done that too
15:05:54 RamananS says " I logged in today an hour early."
15:06:59 ClareS says "Ah"
15:07:37 ClareS says "We always give times in GMT as everyone can always find out where they are in relation to it"
15:08:06 ClareS says "do you have any particular questions or problems on supersecondary structure that you'd like to discuss?"
15:08:35 RamananS says (to ClareS) "But last night when I tried to test my connection from home I could not get through to 'shuna' around 20:00 GMT.I suspect the problem might be with my new ISP"
15:09:47 ClareS says (to RamananS) "did you send an email to Ian Tickle asking if there was a problem?"
15:10:09 ClareS says (to RamananS) "did you try straight telnet as well as the web?"
15:11:26 RamananS says (to ClareS) "I think I tried both protocols.But I did not mail Ian."
15:11:28 KevinO says "with alpha-alpha structures, it seems that there are ridges in"
15:11:35 ClareS says "your new ISP might possibly not be allowing connections to MUDs, I suppose"
15:11:58 KevinO says "in almost any direction"
15:12:09 ClareS says "I suggest you mail Ian and let him know exactly how you were trying to come in and what ISP you were using"
15:12:36 RamananS says (to ClareS) "No last night I was testing my new connections from home few hours in advance."
15:12:48 KevinO says "what makes the +4 ridge more favourable?"
15:13:06 ClareS says (to KevinO) "are you talking about the alpha helix packing page?"
15:13:24 KevinO says (to ClareS) "yes"
15:14:17 KevinO says "it says that there are +4, +3 and +n ridges"
15:14:36 ClareS says "you can (of course) pick out the ridges & grooves from any pattern of residues"
15:16:03 KevinO says "yes, but what makes one pattern more favorable than another?"
15:16:29 KevinO says "... I mean for packing"
15:17:21 ClareS says "the +4 and +3 grooves can be picked out because there are between 3 & 4 residues per turn"
15:17:39 ClareS says "so the ridges of one helix can fit into the grooves of the next"
15:18:01 ClareS says "you could, for example, pick out a +2 ridge"
15:18:25 ClareS says "but it wouldn't be much use.. because the grooves would lie on alternate sides of the helix"
15:18:59 ClareS says "no good for helix-helix packing tho' other small molecules could fit in each groove"
15:19:09 RamananS disconnects.
15:19:09
ClareS PPS HTTP 20m 48s 10s
DavidM PPS HTTP 19m 52s 18m 21s
KevinO PPS HTTP 16m 46s 2m 40s
15:19:10 ClareS says "is that clearer?"
15:19:54 RamananS connects.
15:19:54
RamananS PPS HTTP 0s 0s
ClareS PPS HTTP 21m 33s 44s
DavidM PPS HTTP 20m 37s 19m 6s
KevinO PPS HTTP 17m 31s 3m 25s
15:20:21 KevinO says "well, the +2 example is not that interesting, what about something larger?"
15:20:54 ClareS says "there is another clear explanation in Branden & Tooze"
15:21:32 ClareS says "if you pick every 8 residues (say) you have selected two residues 2 turns apart"
15:21:45 KevinO says "... oh, I guess they need to be prime relative to 3 or 4, but close enough to a multiple of 4"
15:22:34 ClareS says "yes, picking every 8 residues will just give you half the residues in the +4 groove for instance"
15:24:06 ClareS says "it's quite complex... it might help you to find some of those old-fashioned plastic models of helices and try to fit them together"
15:24:46 KevinO says "OK, so say that you pick 7, is there some simple reason why this packs less well than 4?"
15:25:55 KevinO says "sorry for dropping off all the time, netscape is being unfriendly"
15:26:53 ClareS says "if you pick every 7 residues you have picked every other turn, there is a piece of the groove missed out!"
15:28:06 KevinO says "well, that's what I would have thought - but why do the notes"
15:28:06 ClareS says "the 7th residues in an alpha helix do line up in a straight line (every other turn of helix) and these have structural importance..."
15:28:28 KevinO says "that there are +n grooves?"
15:28:35 ClareS says "have you heard of leucine zippers?"
15:28:49 ClareS says "+n is every residue"
15:28:56 KevinO says "yes"
15:29:41 KevinO says "+n is every nth residue, +1 is every residue surely"
15:29:47 ClareS says "a ridge made up of every side chain winds round the outside of the helix"
15:30:23 ClareS says "very tightly -- you couldn't imagine a molecule coiling round like that"
15:30:54 ClareS says "the ridges and grooves exist, they are just not much use for helix-helix packing"
15:32:27 KevinO says "so its not really a very useful observation, in the context of"
15:32:27 ClareS says "or indeed, for packing any other kinds of molecules apart from very small ones"
15:32:46 KevinO says "super-secondary or tertiary structure"
15:34:05 ClareS says "not really... but we thought it was useful to point out that the other grooves exist even tho' you can't pack helices into them"
15:36:18 ClareS says "is this clear?"
15:36:43 KevinO says "yes, thanks"
15:39:12 ClareS says "are there any other questions on this section?"
15:40:12 ClareS looks round expectantly
15:43:20 KevinO says "I don't have anything else at present"
15:44:14 RamananS says "I wish I had gone through all the visualisations on time."
15:45:14 ClareS says "there is still time... the next section won't be released until the 29th"
15:45:31 RamananS says "For now , everything is clear enough."
15:45:34 ClareS says "so you have all of next week to investigate this section further"
15:46:13 ClareS says "(sorry about the delays I was AFK for a few minutes)"
15:46:36 RamananS says "One question:The references- are they all upto date?"
15:47:00 ClareS says "they should be but I am afraid that we don't always add new ones every year"
15:47:51 RamananS says "May be nothing new has been elucidated in these basic concepts in recent times?Am I correct?"
15:49:24 ClareS says "you can certainly get away much better with "classic" references when you are studying basic subjects"
15:49:52 ClareS says "if you have access to the journal Current Opinion in Structural Biology it will give you a good idea of the latest thinking"
15:50:44 ClareS says "but I am almost certain that there will not be much new on supersecondary structure"
15:51:21 ClareS says "or even tertiary or quaternary structure"
15:51:39 ClareS says "there are always new ideas about how proteins fold, and of course there are new folds"
15:52:02 RamananS disconnects.
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ClareS PPS HTTP 53m 41s 23s
DavidM PPS HTTP 52m 45s 24m 49s
KevinO PPS HTTP 49m 39s 8m 42s
15:52:18 RamananS connects.
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RamananS PPS HTTP 0s 0s
ClareS PPS HTTP 53m 57s 39s
DavidM PPS HTTP 53m 1s 25m 5s
KevinO PPS HTTP 49m 55s 8m 58s
15:52:31 KevinO says (to ClareS) "so you are predicting no new motifs?"
15:52:42 ClareS says (to RamananS) "are you having problems with your connection?"
15:53:16 ClareS says (to KevinO) "that depends what you mean by motifs.. probably no new combinations of a few s.s. elements. *Certainly* there will be new folds"
15:54:27 KevinO says (to ClareS) "I'm thinking of things like the Greek key, or 4-helix bundle"
15:55:13 KevinO says (to ClareS) "is there some statistical reason for believing this?"
15:56:00 KevinO says (to ClareS) "or have all the reasonable (small) configurations been enumerated?"
15:56:41 ClareS says "Just that so many proteins have now been crystallised -- there is a limited number of ways in which small numbers of helices and strands can be joined"
15:57:31 ClareS says "many are energetically unfavourable -- it is a reasonable guess that any that haven't been seen in the 12,000 crystal structures we have so far won't be seen in the future"
15:57:57 ClareS says "We don't have a statistically significant sample of solved membrane protein structures yet, tho'"
16:03:29 KevinO says "so how big is the design space?"
16:03:36 ClareS says "I would like to close the meeting quite soon -- are there any other questions before I do?"
16:03:51 ClareS says (to KevinO) "I'm not quite clear what you mean"
16:04:48 KevinO says "oh, I'm trying to understand how you would know what a good"
16:05:24 KevinO says "statistical sample would be."
16:05:37 ClareS says "one example: there are 24 different topologies in which 2 adjacent beta hairpins can be joined"
16:06:01 ClareS says "only 8 have ever been observed and some of those have only been seen once"
16:06:26 ClareS says "clearly those few topologies that are common are much more energetically favourable"
16:07:01 KevinO says "yes, but perhaps that is because nature hasn't found a use for them?"
16:08:07 KevinO says "Perhaps one could design a protein using one of these topologies?"
16:08:50 KevinO says (to ClareS) "anyway, I should let you go (and it IS lunch time)"
16:09:48 ClareS says "possibly, but we are looking at a very large sample of structures"
16:09:54 ClareS says "(now("
16:10:22 ClareS says "if you would like to continue this discussion, do email the PPS discussion list -- that's what it's there for"
16:11:28 KevinO says (to ClareS) "OK, but it doesn't seem to get much use."
16:12:54 ClareS says "it is supposed to be for both announcements and general discussion of protein structure"
16:13:17 ClareS says "but people keep forgetting that it can be used for general discussion -- it would be good to remind them!"
16:15:02 KevinO says "ok, but I need to go now- bye!"
16:15:21 RamananS says "Thank you very much. I have few burning issues (protein str .- computing related) I would like to raise in the pps list.I have to take your leave for now.Thank you and bye."
16:15:30 ClareS says "that's fine, thanks for making it such an interesting meeting"
16:15:33 DavidM says "Thanks, Clare"
16:15:45 ClareS says "I look forward to seeing your posts to the list"
16:15:53 DavidM waves
16:15:59 ClareS says (to KevinO) "enjoy your lunch!"
