MUD transcript: 18-05-00
Tertiary Structure I
Course room(s): PPS
22:01:14 SarahL connects.
LarryT PPS Telnet 13m 41s 2m 50s
StephanieD PPS HTTP 3m 22s 1m 38s
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22:05:06 ClareS connects.
LarryT PPS Telnet 17m 32s 1m 55s
StephanieD PPS HTTP 7m 13s 5m 29s
SarahL PPS HTTP 3m 51s 3m 51s
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22:05:13 ClareS says "Hi everyone"
22:05:33 ClareS says "sorry I'm late.. I hope that no-one has already given up on this meeting"
22:05:50 ClareS blushes
22:06:23 ClareS says "now I'm here at last... how has everyone found section 9?"
22:07:24 SarahL says "hi everyone"
22:07:42 StephanieD says "I must admit ti having found this section one of the most complex...."
22:08:16 ClareS says "it is certainly one of the more complex sections -- the course starts easy and gets harder!"
22:09:44 ClareS says "the terminology used to define protein structure can be rather confusing"
22:11:32 SarahL says "I'm taking it slowly"
22:11:43 ClareS says "does anyone have a particular question they'd like to start with?"
22:11:57 StephanieD says "What level of classification is the term mosaic protein? Would that be classified at quaternary?"
22:12:44 ClareS says (to StephanieD) "no... the term quaternary structure is only used to refer to the association of more than one separate protein chain"
22:14:49 ClareS says "a mosaic protein is one which consists of large numbers of domains joined together in a single chain"
22:15:04 ClareS crashed Netscape in the middle of answering that question :(
22:15:17 ClareS says "there will be more on mosaic proteins in the next section"
22:15:32 StephanieD says "thanks.."
22:17:19 ClareS says "the immunoglobulin domain is one that often occurs in large numbers in a single chain"
22:18:31 StephanieD says "Is it at all possible to determine from the sequence, the likelihood of a particular motif being present?"
22:18:59 ClareS says "that depends on the way the term "motif" is used..."
22:19:38 ClareS says "confusingly, "motif" is used to refer to patterns of residues in sequence that have particular functions"
22:19:42 MichaelS connects.
LarryT PPS Telnet 32m 9s 10m 49s
StephanieD PPS HTTP 21m 50s 1m 11s
SarahL PPS HTTP 18m 28s 8m 10s
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22:19:50 StephanieD says "for example, the heptad repeat pointing to the likelihood of alpha-helical coils. Are there more such examples?"
22:19:58 ClareS says "as well as to combinations of secondary structure elements"
22:20:17 MichaelS says "Hello everyone. Sorry I'm so late."
22:20:34 ClareS says "you can (of course) pick up these functional motifs from their sequences -- do you remember the PROSITE database?"
22:20:53 ClareS says (to MichaelS) "Hello, don't worry... I was late too :("
22:21:16 ClareS says "but some supersecondary structures do have associated sequence patterns"
22:21:47 ClareS says "e.g. the helix turn helix associated with DNA binding has a particular pattern of residues associated with it"
22:22:14 ClareS says "the calcium binding helix turn helix motif (which is a different shape) has a different sequence pattern"
22:22:35 ClareS says (to StephanieD) "do you have a copy of Branden & Tooze?"
22:24:37 SarahL says "I'm waiting for delivery of my Brandon and Tooze it should arrive any day"
22:24:55 StephanieD says "I do..."
22:25:39 ClareS says "chapter 2 has a good discussion of these two kinds of helix-turn-helix and how they can be recognised from sequence patterns"
22:26:27 ClareS says "there is some sequence specificity in beta hairpins but not much"
22:26:47 ClareS says "and beta hairpins also occur in proteins with many diverse *functions*"
22:27:01 ClareS says "is that clearer?"
22:27:42 StephanieD says "Yes thank you"
22:28:50 ClareS crashed netscape again.. this machine is too old!
22:30:22 ClareS says "does anyone else have a question?"
22:31:21 ClareS says "I've just read through that part of the course material and realise you might be confused..."
22:31:56 ClareS says "... the structure that I have been referring to as a calcium-binding helix-turn-helix is the one that Jon Cooper refers to as an E-F hand"
22:32:34 ClareS says "the strange name is because the motif was first seen between the E and F helices of parvalbumin"
22:33:17 ClareS looks round expectantly -- you're all strangely quiet tonight
22:34:01 ClareS says "have any of you given any thought to what kind of project you might want to do"
22:35:23 MichaelS says "As I will be starting a Phd next year, I was thinking of looking at some of the material in it...transcription factors."
22:36:01 LarryT says "I have been considering a "step thru" from sequence to homology based model "cause it's something I've had to do recently and it was an interesting learning experince with some bizarre structures obtained before I got a reasonable model"
22:36:05 SarahL says "how do we set about our projects is there much guidanceor are we just to pick a title"
22:36:29 ClareS says "I can't be sure what will be on the projects list -- but that's such an important subject area that there is almost bound to be something suitable"
22:37:03 ClareS says "you have to pick a title from a list -- but it's a long list"
22:37:37 ClareS says "ranging from discussing a single motif or protein family, to techniques based projects"
22:37:58 StephanieD says "Do you think it likely that there may be immunology -related topics.....or general titles that may be applied to the field?"
22:38:42 ClareS says (to SarahL) "you are not given any specific guidance, but you can always discuss a particular choice with your tutor (or with me)"
22:39:03 ClareS says (to StephanieD) "it's fairly likely -- again that's a wide and important subject area"
22:39:43 ClareS says (to StephanieD) "one of our previous students did an excellent project on the MHC complex"
22:40:14 StephanieD says (to That) "'s good....I was hoping to use the opportunity to read up some molecular immunology"
22:40:59 SarahL says "how long (in words and picture )"should it take up in web space""
22:41:01 ClareS says "we are currently re-writing the end of the course, from next year there will be a whole section devoted to molecular immunology"
22:41:30 ClareS says (to SarahL) "we will point you at some previous good projects for you to get an idea of what is required"
22:42:15 ClareS says (to StephanieD) "have you seen "Immunobiology" by Janeway et al?"
22:42:47 ClareS doesn't usually spend so much of a MUD recommending the products of dead trees :(
22:43:01 StephanieD says "Indeed I have..its an excellent overall introduction"
22:43:50 ClareS has just bought it as a resource for the new section
22:44:19 SarahL says "so it could be on PFEMP-1 the protein expressed on malaria infected redblood cells"
22:45:17 ClareS says (to SarahL) "what do you mean -- you want to do your project on that protein?"
22:47:18 SarahL says "Is that what you can do just choose a protein or does it have to be more specific"
22:47:58 ClareS says (to SarahL) "no -- you have to choose one of the subjects on our list! Most will be more general than just one protein"
22:48:24 ClareS says "but in many cases you will be able to apply the project to something you have worked, or are working on"
22:48:25 StephanieD says "have to leave, I'm afraid. Bye everyone"
22:48:41 ClareS says (to StephanieD) "Bye!"
22:48:51 StephanieD disconnects.
LarryT PPS Telnet 1h 1m 12m 50s
SarahL PPS HTTP 47m 37s 1m 33s
ClareS PPS HTTP 43m 46s 10s
MichaelS PPS HTTP 29m 9s 13m 28s
22:50:18 SarahL says "ok , when will we be able to see the list?"
22:50:54 ClareS says "it should be out early next month"
22:51:26 MichaelS says "So a project on GATA-1 and zinc finger transcription factors would not be out of the question, if it fell into a larger topic area."
22:51:34 ClareS says "project work starts at the beginning of August"
22:52:53 ClareS says "if it did fall into a wider topic area we would expect some coverage of the whole area but you could get away with picking an example for detailed study"
22:53:17 ClareS says "we *have* to guard against people just putting HTML tags round the first chapter of their theses"
22:53:29 ClareS says "the PPS project is a separate piece of work"
22:53:49 ClareS says "tho' of course you all have particular scientific interests and we try to recognise that"
22:54:06 MichaelS says "Fair enough:-)"
22:54:14 SarahL says " no worries there then!"
22:55:28 MichaelS says "I'll be at Sydney University Biochem Dept."
22:55:39 ClareS says "I would like to wind this meeting up fairly soon.. does anyone have any last questions.. on the projects or, of course, on supersecondary structure"
22:55:45 ClareS yawns
22:57:02 MichaelS says "None from me. I'm done in. Godd night all."
22:57:20 SarahL says "will there be a self assessment excercise at the end of section 12"
22:58:08 ClareS says (to SarahL) "yes there will.. and a fiendishly difficult Protein Identification Quiz ;)"
22:59:07 MichaelS disconnects.
LarryT PPS Telnet 1h 11m 9m 3s
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22:59:26 LarryT says "so are you suggesting we memorize all the art work on the R & T CD (g)"
23:00:47 ClareS says (to LarryT) "alexei murzin has done, apparently his brain beats most computer programs in homology modelling ;)"
23:01:34 SarahL says "thats something to look forward to then!- I have actually found the self assessment very useful for consolidation. I found it hard getting the exercise in on time but I was pleased that I did answer the questions eventually"
23:02:16 ClareS says (to SarahL) "are you looking forward to the self assessment or to the quiz?"
23:04:15 ClareS will have to go before she falls asleep -- g'night all!