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MUD transcript:  14-04-00

Protein Secondary Structure

Course room(s): PPS 

21:59:46  ClareS connects.

SarahL       PPS          HTTP    14m 42s  14m 42s
ClareS       PPS          HTTP         0s       0s
21:59:52  ClareS says "Hi"
22:00:24  ClareS says "here at last... the tutorial this afternoon never happened as people forgot the timezone change"
22:01:01  ClareS says "I hope that there will be a few more of us here this evening: I suggest we wait around for a few minutes as it's only *just* 11"
22:01:14  SarahL says "Hi clare  Iwas beginning to think that I had the time wrong!"
22:02:52  ClareS says "no you didn't -- but a lot of people have been making that mistake"
22:03:16  ClareS says "the MUD runs on GMT so it's a lot easier  in the winter"
22:03:41  ClareS says "Sorry I couldn't give you any more notice for these sessions"
22:05:37  SarahL says "are you working away from college at the moment"
22:06:22  ClareS says "I am travelling so much this month that I'm not in Birkbeck at all and this is the only working day I'm at home"
22:08:49  SarahL says "sorry for the delay my computer is on a go slow _just for a change"
22:09:27  VijayK connects.
SarahL       PPS          HTTP    24m 23s      38s
ClareS       PPS          HTTP     9m 41s    3m 5s
VijayK       PPS          HTTP         0s       0s
22:10:50  VijayK says "Hello"
22:10:54  ClareS says (to VijayK) "Hi"
22:11:13  ClareS says "I think it might be good to start now... some people may well arrive later"
22:11:33  VijayK says "Trying to get my act together. had a busy day"
22:11:39  ClareS says "I was apologising to Sarah for having given people such little notice -- I'm away for most of this month"
22:11:46  KevinO connects.
SarahL       PPS          HTTP    26m 42s   2m 57s
ClareS       PPS          HTTP     12m 0s       7s
VijayK       PPS          HTTP     2m 19s      13s
KevinO       PPS          HTTP         0s       0s
22:11:48  ClareS understands only too well
22:12:07  KevinO says "hi all"
22:12:11  ClareS says "How have you found section 8?  Was secondary structure easier the second time round?"
22:12:18  ClareS says (to KevinO) "Hi"
22:12:43  ClareS says "we have only just started properly"
22:13:05  ClareS says (to SarahL) "did you try to zoom in? Or did that fail to work properly too?"
22:13:23  VijayK says "Section 8 makes thigs a bot more lucid. I did not complete the reading"
22:13:59  ClareS says "well you have a long Easter break ahead of you -- with just the next assessment to worry about ;)"
22:14:15  ClareS says "(that should be released on Monday)"
22:14:18  VijayK says "I surely forgot all about zooming in. Will try"
22:15:30  ClareS says "It *should* have appeared on your screen first at a readable size..."
22:15:54  SarahL says "i TRIED ZOOm but that only made them smaller!"
22:15:55  ClareS says "...but at least if you zoom in you will be able to see what the problem is (and hopefully see the helices too)"
22:16:19  ClareS says (to SarahL) "you should be able to zoom in both directions"
22:16:59  VijayK says "A very basic thing - Is the term globular proteins refer to naturally occuring proteins as opposed to other protiens (what are the others?)"
22:17:34  ClareS says "just in case you can't remember, zoom is shift down, left mouse button down, move the mouse up & down (not left to right)"
22:17:50  ClareS has just checked
22:18:24  ClareS says (to VijayK) "globular proteins refers to proteins that are neither fibrous (e.g. collagen) or membrane bound (e.g. rhodopsin)"
22:19:01  SarahL says "how do you do that then?I enter zoom and a number at the rasmol command line"
22:19:18  VijayK says "Does that mean all other proteins exist in a globular form?"
22:19:35  ClareS says "you don't need to bother to use the command line"
22:20:38  ClareS says (to VijayK) "globular proteins are water soluble (ie. soluble in cytoplasm or the extracellular medium or whatever)"
22:21:23  SarahL says "I'll have a go at that then."
22:21:27  ClareS has never tried zoom on the comand line before but agrees with Sarah that it's not very useful
22:21:44  VijayK says "Thank you"
22:23:06  MichaelS connects.
SarahL       PPS          HTTP     38m 2s   1m 43s
ClareS       PPS          HTTP    23m 20s   1m 39s
VijayK       PPS          HTTP    13m 39s   1m 22s
KevinO       PPS          HTTP    11m 20s  10m 59s
MichaelS     PPS          HTTP         0s       0s
22:23:35  ClareS says (to MichaelS) "Hi"
22:24:17  ClareS says "we have been discussing rasmol and the definition of globular proteins"
22:24:33  MichaelS says (to ClareS) "Hello, sorry I'm late, farewell at the local..."
22:25:02  ClareS understands...
22:25:23  ClareS says (to MichaelS) "how have you found section 8?"
22:26:14  VijayK says "About Prediction of Secondary structure - wil l it be a useful topic for individual projects?"
22:26:26  MichaelS says "It has been a good section very full of detail, but pulling different strands together."
22:26:56  ClareS says "I can't say yet -- but there's usually a topic on this kind of theme"
22:27:13  ClareS says (to MichaelS) "did you find it easier second time round?"
22:29:10  ClareS says "most people usually find this section a relief after the mathematics of section 7"
22:29:27  KevinO says "why does the small hole in the pi helix cause a problem"
22:29:49  MichaelS says "I must confess that my time has been so full that I didn't get all of the way through. My previous experience has been in the sections that i didn't reach - NMR etc."
22:30:17  ClareS says (to KevinO) "I'd like to look that up in the course material -- can you post the URL, please?"
22:30:48  ClareS says (to MichaelS) "and we don't give you very long...because it's largely a revision section"
22:31:03  KevinO says "http://pps9900.cryst.bbk.ac.uk/ppscore/section8/ss_9607f.htm"
22:31:08  ClareS says "quite a lot of the material was covered earlier, apart from things like secondary structure prediction"
22:31:15  ClareS says (to KevinO) "thanks"
22:32:01  VijayK says "The figures are very useful to understand the topic all over"
22:32:24  SarahL says "I also have not completed this section, But am finding it interesting and hope that I can remember the information"
22:32:31  ClareS says "I see now... this rare type of helix has a very large radius"
22:33:04  ClareS says "the standard alpha helix has a narrow radius and the interior of the helix is filled with side chains"
22:33:26  ClareS says "those side chains are in van der waals contact with each other, which is energetically favourable"
22:33:53  ClareS says "the pi helix has a hole down the centre which is too large to be filled with side chains"
22:34:11  ClareS says "thus leaving a space which is too small for any molecules, even water molecules"
22:34:32  ClareS says "a larger cavity could be filled with water molecules, which would also be energetically favourable"
22:34:38  KevinO says (to ClareS) "what is the relevance of the statement that solvent molecules can't fit?"
22:34:41  ClareS says "does that make sense?"
22:35:20  ClareS says "you are left with a hole which is too small for anything to fill -- this is energetically unfavourable"
22:36:00  KevinO says (to ClareS) "yes, except my intuition doesn't tell me that the empty hole is energetically unfavorable"
22:36:35  ClareS says "nature abhors a vacuum..."
22:36:44  KevinO says (to ClareS) "... unfavourable, been here too long!"
22:36:46  MichaelS says "Does that mean there is nothing in the central cavity? Or does something very small get in during formation of the helix?"
22:37:08  ClareS says "there is nothing in the centre -- it is too small for any molecule to fit in"
22:37:34  ClareS says "but nevertheless the interior side chains are too far apart to make contact"
22:37:47  ClareS says (to KevinO) "I had no idea you were an expat Brit ;)"
22:37:59  SarahL says "If you look at figure 2 :/pps9900.cryst.bbk.ac.uk/ppscore/section8/ss_96074.htm  you can see the hole down the middle I hadn't noticed that before!"
22:38:24  KevinO says (to ClareS) "yes, Queen Mary College"
22:39:42  ClareS says "that url is unclickable as there are three /s for some reason"
22:40:25  VijayK says "Do I understand thata helix must prferably have no hole at all or if it does it should be able to fit in solvent molecules?"
22:42:03  ClareS says (to VijayK) "exactly! Tho' although there are protein structures that have pores for solvent, they are not strictly speaking helices"
22:42:36  VijayK says "So is Pi helix unstable?"
22:43:31  ClareS says "it is not absolutely unstable but it is energetically unfavourable enough to be extremely rare"
22:43:33  SarahL says "http://pps9900.cryst.bbk.ac.uk./ppscore/section8/ss_96074.htm"
22:44:07  KevinO says "so, all cavities in globular proteins should be large enough to fill with water molecules"
22:44:31  MichaelS says "Have any other roles for pi-helices been proposed, such as seeding sites for alpha-helices etc?"
22:45:52  ClareS says (to KevinO) "that's right"
22:46:53  VijayK says "Where does a pi helix exist, in what conditions?"
22:47:57  ClareS says "if the other interactions around that part of the protein are such that the pi helix is stabilised"
22:48:59  VijayK says "Stabilised by van der vaals forces etc.?"
22:49:33  KevinO says "so, allthough the pi-helix is not in its lowest energy state, the surrounding are is?"
22:49:42  ClareS says "yes, or by electrostatic interactions, hydrogen bonds etc"
22:49:48  ClareS says (to KevinO) "exactly!"
22:50:01  KevinO says "I mean area"
22:50:46  ClareS says (to KevinO) "area??"
22:51:34  KevinO says (to ClareS) "... surrounding area ... is in its lowest energy configuration"
22:52:32  ClareS says (to KevinO) "yes... of course... I somehow guessed you meant that and forgot you hadn't said it exactly"
22:52:41  VijayK says "correction?"
22:52:45  ClareS says "(it's getting late, here at least)"
22:53:34  KevinO says (to ClareS) "yes, almost dinner time!"
22:54:18  VijayK says "Bed time here. Happy Easter"
22:54:19  ClareS had hers hours ago
22:54:46  SarahL says "where are you kevin"
22:55:10  KevinO says "Westchester county, just North of New York City"
22:55:13  ClareS says "that sounds like a good idea -- but does anyone have a final question before we close the tutorial?"
22:57:08  KevinO says "Not I, goodnight!"
22:57:25  VijayK says "The section is short theory wise and revision. Feel wiser now."
22:57:42  ClareS says "excellent!"
22:58:00  MichaelS says "That's all for me."
22:58:26  VijayK says "Thank you Clare and everybody"
22:59:20  ClareS says "Happy Easter -- and don't forget the next set of self-assessment exercises"
22:59:32  ClareS says "they should be appearing on the website on Monday"
22:59:50  SarahL says "thanks everyone have a good Easter"
22:59:52  KevinO says "Happy Easter all, bye"
23:00:09  SarahL says "thanks everyone have a good Easter"
23:00:28  MichaelS says "G'night all."
23:02:43  MichaelS disconnects.