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MUD transcript:  19-05-00

Tertiary Structure I

Course room(s): PPS 

14:58:21  ClareS connects.

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.
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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.
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.
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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.
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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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DavidM       PPS          HTTP    52m 45s  24m 49s
KevinO       PPS          HTTP    49m 39s   8m 42s
15:52:18  RamananS connects.
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!"