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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
SarahL       PPS          HTTP         0s       0s
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
ClareS       PPS          HTTP         0s       0s
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
ClareS       PPS          HTTP    14m 37s       4s
MichaelS     PPS          HTTP         0s       0s
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
SarahL       PPS          HTTP    57m 53s   1m 47s
ClareS       PPS          HTTP     54m 2s      59s
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!